rs13355682

Variant names:

• chr5-180364487-G-A
• rs13355682

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.179 in 152,124 control chromosomes in the GnomAD database, including 2,643 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.18 (2643 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.887

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27128 AN: 152006 Hom.: 2634 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.174

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.179 AC: 27166 AN: 152124 Hom.: 2643 Cov.: 32 AF XY: 0.181 AC XY: 13460 AN XY: 74360

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.183

Alfa AF: 0.159 Hom.: 400

Bravo AF: 0.176

Asia WGS AF: 0.305 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.27
DANN	Benign	0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs13355682; hg19: chr5-179791487;